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Volumn 21, Issue 3, 2014, Pages 311-318

Free energy diagrams for protein function

Author keywords

[No Author keywords available]

Indexed keywords

BETA ARRESTIN; BH3 PROTEIN; CULLIN; G PROTEIN COUPLED RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE P38; NERVE GROWTH FACTOR; PROTEIN; SCAFFOLD PROTEIN;

EID: 84897052340     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2013.12.015     Document Type: Review
Times cited : (27)

References (40)
  • 2
    • 84880353616 scopus 로고    scopus 로고
    • Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate
    • M.N. Bogdał, B. Hat, M. Kochańczyk, and T. Lipniacki Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate BMC Syst. Biol. 7 2013 67
    • (2013) BMC Syst. Biol. , vol.7 , pp. 67
    • Bogdał, M.N.1    Hat, B.2    Kochańczyk, M.3    Lipniacki, T.4
  • 3
    • 77952299611 scopus 로고    scopus 로고
    • The Src, Syk, and Tec family kinases: Distinct types of molecular switches
    • J.M. Bradshaw The Src, Syk, and Tec family kinases: distinct types of molecular switches Cell. Signal. 22 2010 1175 1184
    • (2010) Cell. Signal. , vol.22 , pp. 1175-1184
    • Bradshaw, J.M.1
  • 4
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proc. Natl. Acad. Sci. USA 84 1987 7524 7528
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 5
    • 79953747234 scopus 로고    scopus 로고
    • Cooperativity, local-nonlocal coupling, and nonnative interactions: Principles of protein folding from coarse-grained models
    • H.S. Chan, Z.Q. Zhang, S. Wallin, and Z.R. Liu Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models Annu. Rev. Phys. Chem. 62 2011 301 326
    • (2011) Annu. Rev. Phys. Chem. , vol.62 , pp. 301-326
    • Chan, H.S.1    Zhang, Z.Q.2    Wallin, S.3    Liu, Z.R.4
  • 6
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • K.A. Dill, and H.S. Chan From Levinthal to pathways to funnels Nat. Struct. Biol. 4 1997 10 19
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 7
    • 80053588204 scopus 로고    scopus 로고
    • The energy landscape analysis of cancer mutations in protein kinases
    • A. Dixit, and G.M. Verkhivker The energy landscape analysis of cancer mutations in protein kinases PLoS ONE 6 2011 e26071
    • (2011) PLoS ONE , vol.6 , pp. 26071
    • Dixit, A.1    Verkhivker, G.M.2
  • 9
    • 0032496358 scopus 로고    scopus 로고
    • The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
    • J.E. Ferrell Jr., and E.M. Machleder The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes Science 280 1998 895 898
    • (1998) Science , vol.280 , pp. 895-898
    • Ferrell, Jr.J.E.1    Machleder, E.M.2
  • 10
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • H. Frauenfelder, S.G. Sligar, and P.G. Wolynes The energy landscapes and motions of proteins Science 254 1991 1598 1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 11
    • 6344219895 scopus 로고    scopus 로고
    • Is allostery an intrinsic property of all dynamic proteins?
    • K. Gunasekaran, B.Y. Ma, and R. Nussinov Is allostery an intrinsic property of all dynamic proteins? Proteins 57 2004 433 443
    • (2004) Proteins , vol.57 , pp. 433-443
    • Gunasekaran, K.1    Ma, B.Y.2    Nussinov, R.3
  • 12
    • 84864449930 scopus 로고    scopus 로고
    • Protein frustratometer: A tool to localize energetic frustration in protein molecules
    • M. Jenik, R.G. Parra, L.G. Radusky, A. Turjanski, P.G. Wolynes, and D.U. Ferreiro Protein frustratometer: a tool to localize energetic frustration in protein molecules Nucleic Acids Res. 40 Web Server issue 2012 W348 W351
    • (2012) Nucleic Acids Res. , vol.40 , Issue.WEB SERVER ISSUE
    • Jenik, M.1    Parra, R.G.2    Radusky, L.G.3    Turjanski, A.4    Wolynes, P.G.5    Ferreiro, D.U.6
  • 13
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • S. Kumar, B.Y. Ma, C.J. Tsai, N. Sinha, and R. Nussinov Folding and binding cascades: dynamic landscapes and population shifts Protein Sci. 9 2000 10 19
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.Y.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 14
    • 0026723063 scopus 로고
    • Protein folding funnels: A kinetic approach to the sequence-structure relationship
    • P.E. Leopold, M. Montal, and J.N. Onuchic Protein folding funnels: a kinetic approach to the sequence-structure relationship Proc. Natl. Acad. Sci. USA 89 1992 8721 8725
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 15
    • 64649094816 scopus 로고    scopus 로고
    • KSR1 modulates the sensitivity of mitogen-activated protein kinase pathway activation in T cells without altering fundamental system outputs
    • J. Lin, A. Harding, E. Giurisato, and A.S. Shaw KSR1 modulates the sensitivity of mitogen-activated protein kinase pathway activation in T cells without altering fundamental system outputs Mol. Cell. Biol. 29 2009 2082 2091
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 2082-2091
    • Lin, J.1    Harding, A.2    Giurisato, E.3    Shaw, A.S.4
  • 18
    • 18944374155 scopus 로고    scopus 로고
    • Graded mitogen-activated protein kinase activity precedes switch-like c-Fos induction in mammalian cells
    • J.P. Mackeigan, L.O. Murphy, C.A. Dimitri, and J. Blenis Graded mitogen-activated protein kinase activity precedes switch-like c-Fos induction in mammalian cells Mol. Cell. Biol. 25 2005 4676 4682
    • (2005) Mol. Cell. Biol. , vol.25 , pp. 4676-4682
    • Mackeigan, J.P.1    Murphy, L.O.2    Dimitri, C.A.3    Blenis, J.4
  • 19
    • 0023358977 scopus 로고
    • Mutant sequences as probes of protein folding mechanisms
    • C.R. Matthews, and M.R. Hurle Mutant sequences as probes of protein folding mechanisms Bioessays 6 1987 254 257
    • (1987) Bioessays , vol.6 , pp. 254-257
    • Matthews, C.R.1    Hurle, M.R.2
  • 20
    • 84868619337 scopus 로고    scopus 로고
    • Genetic programs constructed from layered logic gates in single cells
    • T.S. Moon, C.B. Lou, A. Tamsir, B.C. Stanton, and C.A. Voigt Genetic programs constructed from layered logic gates in single cells Nature 491 2012 249 253
    • (2012) Nature , vol.491 , pp. 249-253
    • Moon, T.S.1    Lou, C.B.2    Tamsir, A.3    Stanton, B.C.4    Voigt, C.A.5
  • 21
    • 4143110020 scopus 로고    scopus 로고
    • Hysteresis vs graded responses: The connections make all the difference
    • A.J. Ninfa, and A.E. Mayo Hysteresis vs. graded responses: the connections make all the difference Sci. STKE 2004 2004 pe20
    • (2004) Sci. STKE , vol.2004 , pp. 20
    • Ninfa, A.J.1    Mayo, A.E.2
  • 22
    • 84881493915 scopus 로고    scopus 로고
    • The spatial structure of cell signaling systems
    • R. Nussinov The spatial structure of cell signaling systems Phys. Biol. 10 4 2013 045004
    • (2013) Phys. Biol. , vol.10 , Issue.4 , pp. 045004
    • Nussinov, R.1
  • 23
    • 84876266689 scopus 로고    scopus 로고
    • Allostery in disease and in drug discovery
    • R. Nussinov, and C.-J. Tsai Allostery in disease and in drug discovery Cell 153 2013 293 305
    • (2013) Cell , vol.153 , pp. 293-305
    • Nussinov, R.1    Tsai, C.-J.2
  • 24
    • 84876296757 scopus 로고    scopus 로고
    • A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery
    • R. Nussinov, B. Ma, and C.-J. Tsai A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery Biochim. Biophys. Acta 1834 2013 820 829
    • (2013) Biochim. Biophys. Acta , vol.1834 , pp. 820-829
    • Nussinov, R.1    Ma, B.2    Tsai, C.-J.3
  • 25
    • 84876275408 scopus 로고    scopus 로고
    • The underappreciated role of allostery in the cellular network
    • R. Nussinov, C.J. Tsai, and B. Ma The underappreciated role of allostery in the cellular network Annu. Rev. Biophys. 42 2013 169 189
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 169-189
    • Nussinov, R.1    Tsai, C.J.2    Ma, B.3
  • 28
    • 84865342852 scopus 로고    scopus 로고
    • Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling
    • C.Q. Pan, M. Sudol, M. Sheetz, and B.C. Low Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling Cell. Signal. 24 2012 2143 2165
    • (2012) Cell. Signal. , vol.24 , pp. 2143-2165
    • Pan, C.Q.1    Sudol, M.2    Sheetz, M.3    Low, B.C.4
  • 29
    • 0036531884 scopus 로고    scopus 로고
    • How signaling proteins integrate multiple inputs: A comparison of N-WASP and Cdk2
    • K.E. Prehoda, and W.A. Lim How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2 Curr. Opin. Cell Biol. 14 2002 149 154
    • (2002) Curr. Opin. Cell Biol. , vol.14 , pp. 149-154
    • Prehoda, K.E.1    Lim, W.A.2
  • 31
    • 0033887401 scopus 로고    scopus 로고
    • Early ribbon drawings of proteins
    • J.S. Richardson Early ribbon drawings of proteins Nat. Struct. Biol. 7 2000 624 625
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 624-625
    • Richardson, J.S.1
  • 32
    • 33847355217 scopus 로고    scopus 로고
    • Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
    • S.D.M. Santos, P.J. Verveer, and P.I.H. Bastiaens Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate Nat. Cell Biol. 9 2007 324 330
    • (2007) Nat. Cell Biol. , vol.9 , pp. 324-330
    • Santos, S.D.M.1    Verveer, P.J.2    Bastiaens, P.I.H.3
  • 33
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • T.D. Schneider, and R.M. Stephens Sequence logos: a new way to display consensus sequences Nucleic Acids Res. 18 1990 6097 6100
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 35
    • 49649109812 scopus 로고    scopus 로고
    • Membrane localization of scaffold proteins promotes graded signaling in the yeast MAP kinase cascade
    • S. Takahashi, and P.M. Pryciak Membrane localization of scaffold proteins promotes graded signaling in the yeast MAP kinase cascade Curr. Biol. 18 2008 1184 1191
    • (2008) Curr. Biol. , vol.18 , pp. 1184-1191
    • Takahashi, S.1    Pryciak, P.M.2
  • 36
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • C.J. Tsai, S. Kumar, B.Y. Ma, and R. Nussinov Folding funnels, binding funnels, and protein function Protein Sci. 8 1999 1181 1190
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.Y.3    Nussinov, R.4
  • 37
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • C.J. Tsai, B.Y. Ma, and R. Nussinov Folding and binding cascades: shifts in energy landscapes Proc. Natl. Acad. Sci. USA 96 1999 9970 9972
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.Y.2    Nussinov, R.3
  • 38
    • 8644266706 scopus 로고    scopus 로고
    • Stimulus-coupled spatial restriction of extracellular signal-regulated kinase 1/2 activity contributes to the specificity of signal-response pathways
    • A. Whitehurst, M.H. Cobb, and M.A. White Stimulus-coupled spatial restriction of extracellular signal-regulated kinase 1/2 activity contributes to the specificity of signal-response pathways Mol. Cell. Biol. 24 2004 10145 10150
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 10145-10150
    • Whitehurst, A.1    Cobb, M.H.2    White, M.A.3
  • 40
    • 0345359924 scopus 로고    scopus 로고
    • A positive-feedback-based bistable 'memory module' that governs a cell fate decision
    • W. Xiong, and J.E. Ferrell Jr. A positive-feedback-based bistable 'memory module' that governs a cell fate decision Nature 426 2003 460 465
    • (2003) Nature , vol.426 , pp. 460-465
    • Xiong, W.1    Ferrell, Jr.J.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.